For my Diplom and Master's Thesis my research centered on translational control. In inserted control elements into reporter mRNA and tested their translational efficiency and stability in animal, plant, and fungi systems. I also modified the CAP, poly-A tail, and leader sequences to test their influence on the control elements.
For my Master's Thesis I analyzed the 5' leader sequence of the tobacco etch virus to identify the sequences that allows for efficient translation of poly-adenylated mRNA in the absence of a cap structure. I identified two cap-independent regulator elements that promote cap-independent and translation as well as intercistronic translation initiation. Surprisingly I also found that a strong secondary structure at the 5'-proximal regulatory element markedly decreases translation suggesting that, even though the 5' leader does promote intercistronic initiation, translation is much more efficient when initiated from a free 5' end.
For my Diplom Thesis I tested how strong secondary structure in the 5' and 3' ends of mRNA affects translation efficiency in plant, animal, and fungi systems. While secondary structure significantly reduced the overall protein yield from a reporter mRNA, dependent both on the exact location of the secondary structure and its stability. The interaction between the poly-A tail and the cap of the mRNA were not affected. This suggests that even though ribosomes either pause or slow down during the process of melting the secondary structure, they do not dissociate from the mRNA, thus allowing reinitiation of mRNA circularized by the cap/poly-A tail interaction.
Niepel, M, J Ling, and DR Gallie. “Secondary structure in the 5'-leader or 3'-untranslated region reduces protein yield but does not affect the functional interaction between the 5'-cap and the poly(A) tail.” FEBS letters 462, no. 1-2 (1999): 79 - 84.
Niepel, M, and DR Gallie. “Identification and characterization of the functional elements within the tobacco etch virus 5' leader required for cap-independent translation.” Journal of virology 73, no. 11 (1999): 9080 - 8.